Research workbench
Crystal structure of mltc in complex with disaccharide pentapeptide DHL89
Analyse Crystal structure of mltc in complex with disaccharide pentapeptide DHL89 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4CHX
- Type
- protein
- Length
- 658 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Membrane-bound lytic murein transglycosylase C; Nag-anhmur-pentapeptide
- EC
- 4.2.2.-
- UniProt
- C5A0N2
- Ligands
- AH0, API, NAG
- Pockets
- 8 · best druggability 0.66
Structure
x-ray diffraction · 2 distinct chains · 51% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Membrane-bound lytic murein transglycosylase C (EC 4.2.2.-) | protein | 327 | 52% helix, 13% strand | C5A0N2 |
| C | Nag-anhmur-pentapeptide | protein | 4 | 0% helix, 0% strand | — |
Ligands and binding sites
- AH0 · 2-(2-acetylamino-4-hydroxy-6,8-dioxa-bicyclo[3.2.1]oct-3-yloxy)-propionic acid · ligand · chains A, C
- API · 2,6-diaminopimelic acid · ligand · chains A, C
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 52 | 0.66 | 0.96 | 17 | empty |
| 2 | 485 | 0.64 | 0.77 | 35 | empty |
| 3 | 194 | 0.54 | 0.78 | 27 | NAG, AH0 |
| 4 | 180 | 0.48 | 0.76 | 28 | empty |
| 5 | 93 | 0.46 | 0.80 | 14 | empty |
Interfaces
2 interfaces between chains.
- A–B · 458 Ų buried · 9 hydrogen bonds · protein-protein
- A–C · 376 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 covalent, 3 d-amino (covalent ligand, D-amino acid).
Compared structures
- 4CHX · Crystal structure of MltC in complex with disaccharide pentapeptide DHl89 · the same entry in another collection · chain A against A, TM-score 1.00
- C5A0N2 · AlphaFold monomer V2.0 prediction for membrane-bound lytic murein transglycosylase C… · a predicted model of the same protein · chain A against A, TM-score 0.99
Analyse
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Every structure of UniProt C5A0N2
- Elsewhere: RCSB PDB 4CHX · PDBe 4CHX · UniProt C5A0N2
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.